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GeneBe

3-186853103-T-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_004797.4(ADIPOQ):c.45T>G(p.Gly15=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 1,614,010 control chromosomes in the GnomAD database, including 13,827 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.11 ( 1139 hom., cov: 32)
Exomes 𝑓: 0.12 ( 12688 hom. )

Consequence

ADIPOQ
NM_004797.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.387
Variant links:
Genes affected
ADIPOQ (HGNC:13633): (adiponectin, C1Q and collagen domain containing) This gene is expressed in adipose tissue exclusively. It encodes a protein with similarity to collagens X and VIII and complement factor C1q. The encoded protein circulates in the plasma and is involved with metabolic and hormonal processes. Mutations in this gene are associated with adiponectin deficiency. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Apr 2010]
ADIPOQ-AS1 (HGNC:40648): (ADIPOQ antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.387 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ADIPOQNM_004797.4 linkuse as main transcriptc.45T>G p.Gly15= synonymous_variant 2/3 ENST00000320741.7
ADIPOQ-AS1NR_046662.2 linkuse as main transcriptn.2355A>C non_coding_transcript_exon_variant 4/4
ADIPOQNM_001177800.2 linkuse as main transcriptc.45T>G p.Gly15= synonymous_variant 3/4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ADIPOQENST00000320741.7 linkuse as main transcriptc.45T>G p.Gly15= synonymous_variant 2/31 NM_004797.4 P1
ADIPOQENST00000444204.2 linkuse as main transcriptc.45T>G p.Gly15= synonymous_variant 3/41 P1
ADIPOQ-AS1ENST00000422718.1 linkuse as main transcriptn.2226A>C non_coding_transcript_exon_variant 3/35

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.107
AC:
16297
AN:
152042
Hom.:
1141
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0469
Gnomad AMI
AF:
0.0735
Gnomad AMR
AF:
0.185
Gnomad ASJ
AF:
0.207
Gnomad EAS
AF:
0.294
Gnomad SAS
AF:
0.133
Gnomad FIN
AF:
0.0499
Gnomad MID
AF:
0.269
Gnomad NFE
AF:
0.112
Gnomad OTH
AF:
0.161
GnomAD3 exomes
AF:
0.135
AC:
33830
AN:
251118
Hom.:
2832
AF XY:
0.135
AC XY:
18309
AN XY:
135746
show subpopulations
Gnomad AFR exome
AF:
0.0427
Gnomad AMR exome
AF:
0.187
Gnomad ASJ exome
AF:
0.199
Gnomad EAS exome
AF:
0.301
Gnomad SAS exome
AF:
0.133
Gnomad FIN exome
AF:
0.0511
Gnomad NFE exome
AF:
0.115
Gnomad OTH exome
AF:
0.140
GnomAD4 exome
AF:
0.124
AC:
181897
AN:
1461850
Hom.:
12688
Cov.:
32
AF XY:
0.125
AC XY:
90730
AN XY:
727226
show subpopulations
Gnomad4 AFR exome
AF:
0.0431
Gnomad4 AMR exome
AF:
0.183
Gnomad4 ASJ exome
AF:
0.206
Gnomad4 EAS exome
AF:
0.297
Gnomad4 SAS exome
AF:
0.128
Gnomad4 FIN exome
AF:
0.0521
Gnomad4 NFE exome
AF:
0.118
Gnomad4 OTH exome
AF:
0.139
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.107
AC:
16300
AN:
152160
Hom.:
1139
Cov.:
32
AF XY:
0.109
AC XY:
8131
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.0469
Gnomad4 AMR
AF:
0.185
Gnomad4 ASJ
AF:
0.207
Gnomad4 EAS
AF:
0.293
Gnomad4 SAS
AF:
0.133
Gnomad4 FIN
AF:
0.0499
Gnomad4 NFE
AF:
0.112
Gnomad4 OTH
AF:
0.162
Alfa
AF:
0.103
Hom.:
533
Bravo
AF:
0.115
Asia WGS
AF:
0.210
AC:
728
AN:
3478
EpiCase
AF:
0.129
EpiControl
AF:
0.136

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

ADIPOQ-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesOct 30, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
Cadd
Benign
3.1
Dann
Benign
0.50

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2241766; hg19: chr3-186570892; COSMIC: COSV57859918; API